Contacts of the helix formed by residues 261 - 277 (chain A) in PDB entry 1M2O
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 261 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A TYR* 3.7 6.7 - - - -
163A GLY 2.9 17.0 + - - +
164A ASN 4.3 2.0 - - - +
166A VAL* 4.2 2.0 - - + +
184A GLY* 3.0 45.8 - - - +
259A LEU 4.1 0.4 - - - -
260A ARG* 1.3 68.9 - - - +
262A THR* 1.3 63.7 + - - +
263A GLY 3.2 3.4 - - - +
264A SER* 3.3 2.4 + - - -
265A ALA* 3.1 21.5 + - - +
294A VAL* 3.8 15.7 - - + +
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Residues in contact with THR 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A TYR* 2.9 30.9 + - + +
260A ARG* 3.3 20.1 + - - +
261A ALA* 1.3 71.8 - - - +
263A GLY* 1.3 66.4 + - - +
265A ALA* 3.8 0.2 - - - +
266A LEU* 3.0 32.1 + - + +
286A LEU* 3.7 26.9 - - + -
288A ALA* 5.2 3.3 - - + +
290A GLY 4.7 1.7 + - - -
291A PRO 4.7 0.3 - - - -
292A GLY* 3.9 13.4 + - - -
329A TYR* 4.1 11.4 - - - +
358A MET* 4.7 9.6 - - + -
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Residues in contact with GLY 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A ALA 3.2 0.8 - - - -
262A THR* 1.3 81.3 - - - +
264A SER* 1.3 56.7 + - - +
266A LEU* 3.4 1.7 + - - +
267A ASN* 2.9 27.5 + - - +
296A PRO* 3.1 22.3 + - - -
297A GLY 4.5 0.8 + - - -
328A PHE* 3.6 26.9 - - - -
329A TYR* 3.6 12.2 + - - -
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Residues in contact with SER 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A VAL* 3.4 8.3 - - - +
183A ARG 2.9 20.8 + - - -
184A GLY* 3.5 27.8 - - - -
186A ARG 4.0 11.2 + - - -
261A ALA* 3.3 7.2 + - - +
262A THR 3.3 0.4 - - - -
263A GLY* 1.3 74.1 - - - +
265A ALA* 1.3 59.3 + - - +
267A ASN* 3.2 7.1 + - - +
268A ILE* 2.9 42.5 + - - +
296A PRO* 4.0 9.9 + - - +
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Residues in contact with ALA 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A VAL* 3.8 12.6 - - + +
160A ILE* 3.9 8.6 - - + +
162A TYR* 3.6 40.8 - - + -
166A VAL* 3.7 13.6 - - + +
261A ALA 3.1 11.3 + - - +
262A THR 3.2 4.7 + - - +
264A SER* 1.3 76.0 + - - +
266A LEU* 1.3 59.3 + - + +
268A ILE* 3.5 3.7 + - - +
269A ALA* 3.0 27.4 + - - +
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Residues in contact with LEU 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A VAL* 4.7 3.8 - - + -
262A THR* 3.0 22.6 + - + +
263A GLY* 3.9 2.9 - - - +
265A ALA* 1.3 75.0 - - - +
267A ASN* 1.3 59.5 + - - +
269A ALA* 3.6 2.8 - - - +
270A SER* 2.9 32.3 + - - -
284A ILE* 4.4 20.9 - - + +
286A LEU* 3.9 43.7 - - + -
329A TYR* 4.1 16.8 - - + -
332A ILE* 4.4 13.6 - - + +
343A VAL* 4.9 9.4 - - + -
358A MET* 4.9 1.3 - - - -
361A LEU* 3.7 29.6 - - + -
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Residues in contact with ASN 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A ARG 5.0 1.0 + - - -
187A GLU* 3.9 18.1 - - + +
188A TYR* 3.0 42.1 + - - +
263A GLY 2.9 18.0 + - - +
264A SER* 3.2 8.4 + - - +
266A LEU* 1.3 78.3 - - - +
268A ILE* 1.3 65.6 + - - +
270A SER* 3.1 7.0 + - - -
271A LEU* 3.0 28.2 + - - +
296A PRO* 6.0 0.2 - - + -
328A PHE* 4.3 8.5 - - + -
332A ILE* 3.9 9.2 - - - +
335A ARG* 2.9 32.0 + - - +
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Residues in contact with ILE 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A ILE* 4.3 13.9 - - + -
166A VAL* 4.0 15.7 - - + -
168A LEU* 5.0 8.7 - - + -
182A PHE* 4.2 25.8 - - + -
188A TYR* 3.7 33.4 - - + -
193A LEU* 3.7 30.4 - - + +
264A SER* 2.9 32.0 + - - +
265A ALA* 3.7 4.9 - - - +
267A ASN* 1.3 79.9 - - - +
269A ALA* 1.3 58.6 + - - +
271A LEU* 3.8 1.8 - - - +
272A LEU* 2.9 29.8 + - + +
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Residues in contact with ALA 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A PHE* 3.7 25.0 - - + -
127A VAL* 4.4 3.6 - - + -
160A ILE* 4.2 6.2 - - + +
265A ALA 3.0 18.6 + - - +
266A LEU* 3.6 6.3 - - - +
268A ILE* 1.3 79.3 - - - +
270A SER* 1.3 63.4 + - - +
272A LEU* 3.3 1.9 + - - +
273A LEU* 3.2 23.6 + - - +
284A ILE* 3.7 31.0 - - + -
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Residues in contact with SER 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A LEU 2.9 23.8 + - - -
267A ASN* 3.1 1.7 + - - -
269A ALA* 1.3 73.5 - - - +
271A LEU* 1.3 59.6 + - - +
273A LEU* 3.6 3.1 + - - +
274A GLN* 3.1 23.2 + - - +
284A ILE* 4.0 11.1 - - - +
332A ILE* 3.9 8.7 - - - +
335A ARG* 2.7 44.7 + - - -
336A VAL* 3.8 22.4 - - - -
339A ASN* 4.4 2.4 - - - +
341A HIS* 4.8 1.4 + - - -
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Residues in contact with LEU 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A TYR* 3.3 27.8 - - + +
189A GLN* 3.5 5.2 - - - +
190A LEU* 3.4 49.5 - - + +
193A LEU* 4.4 17.7 - - + -
267A ASN* 3.0 25.0 + - - +
268A ILE 3.9 2.7 - - - +
270A SER* 1.3 74.9 + - - +
272A LEU* 1.3 61.2 + - - +
274A GLN* 3.2 11.5 + - - +
275A GLY* 3.0 23.4 + - - -
335A ARG* 3.5 33.0 - - - +
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Residues in contact with LEU 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A PHE* 4.0 5.6 - - + -
168A LEU* 3.5 39.7 - - + -
193A LEU* 4.2 9.8 - - + +
197A LEU* 4.0 11.4 - - + -
224A LEU* 3.9 34.3 - - + +
227A PHE* 4.1 13.9 - - + -
228A PHE* 3.7 26.2 - - + -
268A ILE* 2.9 20.8 + - + +
269A ALA 3.8 3.6 - - - +
271A LEU* 1.3 77.5 - - - +
273A LEU* 1.3 60.1 + - - +
275A GLY* 3.4 7.6 + - - -
276A CYS* 3.3 21.2 + - - -
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Residues in contact with LEU 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A ILE* 4.3 4.5 - - + -
125A PHE* 4.2 9.0 - - + -
228A PHE* 3.5 32.8 - - + -
269A ALA 3.2 14.6 + - - +
270A SER* 4.1 2.2 - - - +
272A LEU* 1.3 74.4 - - - +
274A GLN* 1.3 59.7 + - - +
277A TYR* 2.7 59.7 + - + +
282A ALA* 3.4 32.5 - - + -
284A ILE* 3.8 28.9 - - + -
341A HIS* 3.3 20.4 - - + +
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Residues in contact with GLN 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A LEU* 3.3 27.7 - - + +
270A SER 3.1 16.6 + - - +
271A LEU* 3.2 12.3 + - - +
273A LEU* 1.3 77.8 - - - +
275A GLY* 1.3 61.5 + - - +
278A LYS* 3.5 33.1 - - + +
335A ARG* 3.4 22.3 + - - +
339A ASN* 3.2 34.6 + - - +
341A HIS* 4.0 3.8 - - - -
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Residues in contact with GLY 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A LEU* 4.1 13.9 - - - +
194A THR* 5.3 0.4 - - - -
224A LEU* 3.8 21.1 - - - +
271A LEU 3.0 14.7 + - - -
272A LEU 3.4 3.5 + - - -
273A LEU 3.2 0.6 - - - -
274A GLN* 1.3 79.7 - - - +
276A CYS* 1.3 58.8 + - - +
278A LYS 5.3 0.2 - - - -
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Residues in contact with CYS 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A LEU* 3.7 29.8 - - + -
225A ASN* 3.8 18.7 - - - +
228A PHE* 3.7 17.9 - - - -
272A LEU 3.3 16.5 + - - -
273A LEU* 4.6 0.4 - - - -
275A GLY* 1.3 78.3 - - - +
277A TYR* 1.3 92.7 + - + +
278A LYS 3.8 1.8 - - - -
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Residues in contact with TYR 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A VAL* 4.1 19.0 - - + +
123A ILE* 3.5 31.0 - - + -
156A LEU* 3.0 26.5 - - + +
225A ASN* 4.5 17.3 + - - +
228A PHE* 3.8 26.9 + + + -
273A LEU* 2.7 31.9 + - + +
276A CYS* 1.3 100.5 - - + +
278A LYS* 1.3 60.8 + - - +
280A ILE* 3.2 27.9 + - + +
341A HIS* 2.6 28.6 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il